Neighbor Optimization RPE¶
This Jupyter notebook (05.02) details the analysis steps to optimize the nearest neighbor analysis.
THIS ANALYSIS STEP DOES NOT OUTPUT AN H5AD FILE.
Initialize Environment¶
First import all the necessary packages here:
InĀ [1]:
# Import necessary packages
import os
import scanpy as sc
import numpy as np
import pandas as pd
import anndata as ad
from datetime import datetime as dt
# Scanpy settings
sc.settings.verbosity = 3
sc.logging.print_header()
# Set working directory
os.chdir("/home/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization")
adata = "01_25-12-05-17-25_preprocessing_RPE.h5ad"
2025-12-05 22:40:10.192293: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations. To enable the following instructions: SSE4.1 SSE4.2 AVX AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
scanpy==1.9.5 anndata==0.10.2 umap==0.5.4 numpy==1.24.4 scipy==1.11.3 pandas==2.1.1 scikit-learn==1.3.1 statsmodels==0.14.0 igraph==0.11.2 louvain==0.8.1 pynndescent==0.5.10
Identify the starting directory. Get a timestamp for the run.
InĀ [2]:
# Determine work location
print("The work location for this notebook is: " + os.getcwd() + "\n")
# Get a timestamp for the start of the run
timestamp = dt.now()
print("This notebook was last run on " + timestamp.strftime("%y-%m-%d %H:%M") + "\n")
The work location for this notebook is: /blue/m.pipkin/dalbao/2023-012-Runx3mutD8scRNA/AlbaoRunx3Manuscript/single_cell/02_optimization This notebook was last run on 25-12-05 22:40
The work directory is structured to contain a folder named "h5ad" which itself contains output from previous analysis steps. Import data from the latest analysis:
InĀ [3]:
# List items in outs folder
adata = ad.read_h5ad("../../h5ad/" + adata)
# Inspect AnnData
print(adata)
AnnData object with n_obs Ć n_vars = 16314 Ć 18505
obs: 'experiment', 'group', 'timepoint', 'infection', 'cell_id', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'total_counts_ribo', 'log1p_total_counts_ribo', 'pct_counts_ribo', 'doublet_score', 'predicted_doublet', 'scDblFinder_score', 'scDblFinder_class', 'gem', 'QC', 'n_genes', 'S_score', 'G2M_score', 'phase'
var: 'mt', 'ribo', 'n_cells_by_counts-gem1', 'mean_counts-gem1', 'log1p_mean_counts-gem1', 'pct_dropout_by_counts-gem1', 'total_counts-gem1', 'log1p_total_counts-gem1', 'n_cells_by_counts-gem2', 'mean_counts-gem2', 'log1p_mean_counts-gem2', 'pct_dropout_by_counts-gem2', 'total_counts-gem2', 'log1p_total_counts-gem2', 'n_cells', 'n_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'group_colors', 'hvg', 'log1p', 'pca'
obsm: 'X_pca'
varm: 'PCs'
layers: 'counts', 'soupX_counts'
Optimize Nearest Neighbors¶
Write a function to automate iteration of nearest neighbor analysis:
InĀ [4]:
# Define a function to automate the iteration of different neighbor values, holding PC constant.
def iterate_neighbors(adata_local, pcs = 25, neighbors = 10, min = 0, max = 11):
# Loop over different nearest neighbor values based on provided min and max values
for index in range(min, max):
# Calculate nearest neighbors with n_neighbors of neighbors + index
adata_mod = sc.pp.neighbors(adata_local, n_neighbors = neighbors + index, n_pcs = pcs, copy = True)
# Do leiden clustering from neighborhood graph
sc.tl.leiden(adata_mod)
# Initialize the PAGA
sc.tl.paga(adata_mod)
sc.pl.paga(adata_mod, title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
# Do a UMAP based on initialized PAGA graph
sc.tl.umap(adata_mod, init_pos='paga')
# Plot UMAP annotated by leiden clusters and original identity
sc.pl.umap(adata_mod, color = "group", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
sc.pl.umap(adata_mod, color = "leiden", title = "neighbor " + str(neighbors + index) + " pcs " + str(pcs))
# Get leiden clusters and original identities
obs_df = sc.get.obs_df(adata_mod, ["group", "leiden"])
# Print tapply
print(obs_df.groupby("group").value_counts().unstack())
del(adata_mod) # Cleanup
# End of loop
del(adata_local)
# End of function
25 PCs, neigbhor 3 to 18¶
InĀ [5]:
iterate_neighbors(adata, pcs = 25, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:14)
running Leiden clustering
finished: found 52 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:03)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 42 43 44 45 \ group ... Base 163 326 1 255 189 18 11 297 18 194 ... 46 4 0 12 Naive 0 0 0 0 0 0 0 1 0 0 ... 0 1 0 0 Null 586 230 0 270 401 0 0 154 33 248 ... 11 11 0 10 WT 41 113 657 59 45 620 595 29 24 40 ... 5 8 0 18 d5 6 25 5 14 8 7 2 12 430 24 ... 0 37 46 0 d8 49 104 0 64 9 3 1 111 75 64 ... 32 15 0 6 leiden 46 47 48 49 50 51 group Base 18 22 0 0 0 0 Naive 0 0 0 0 3 0 Null 14 1 0 0 0 0 WT 5 4 0 0 0 0 d5 0 0 9 7 0 3 d8 4 1 0 0 0 0 [6 rows x 52 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 24 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 14 15 \ group ... Base 315 212 8 662 424 0 37 394 342 23 ... 196 7 Naive 0 0 0 0 0 0 0 1 0 0 ... 0 0 Null 815 896 1 263 495 0 6 194 318 21 ... 74 1 WT 67 44 1157 148 89 1096 846 51 58 28 ... 22 519 d5 3 12 3 7 30 5 12 12 8 647 ... 13 15 d8 114 29 1 74 89 0 5 172 66 45 ... 304 1 leiden 16 17 18 19 20 21 22 23 group Base 0 194 237 149 24 2 0 20 Naive 542 0 0 0 0 1 0 0 Null 0 37 99 60 27 11 0 13 WT 0 237 20 86 24 8 0 5 d5 0 15 12 3 0 40 72 0 d8 0 18 34 23 20 12 0 3 [6 rows x 24 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 19 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 9 583 20 355 776 506 118 530 387 477 22 0 194 Naive 0 0 0 0 0 0 0 0 0 1 0 542 0 Null 2 664 4 1045 330 546 974 299 257 297 19 0 19 WT 1902 183 1622 78 137 86 52 61 63 77 29 0 303 d5 10 56 20 5 9 9 4 16 14 23 659 0 13 d8 1 191 3 74 79 159 17 134 305 147 49 0 6 leiden 13 14 15 16 17 18 group Base 165 0 3 2 30 20 Naive 0 0 0 1 0 0 Null 57 0 1 11 19 21 WT 112 0 74 8 18 25 d5 3 82 2 43 1 0 d8 25 0 1 13 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 19 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 743 333 2 665 572 9 545 487 15 16 280 63 215 Naive 0 0 0 0 0 0 0 1 0 0 0 0 0 Null 765 1203 0 743 345 3 364 269 3 22 53 468 195 WT 199 85 1589 121 78 1242 61 76 792 27 381 25 20 d5 48 4 11 9 16 9 12 19 11 660 19 7 7 d8 205 92 1 55 391 1 67 141 0 49 19 12 129 leiden 13 14 15 16 17 18 group Base 0 196 3 0 33 20 Naive 542 0 1 0 0 0 Null 0 84 12 0 18 18 WT 0 90 8 2 13 21 d5 0 2 54 79 2 0 d8 0 29 13 0 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 4 753 898 93 25 577 534 416 475 18 0 264 86 Naive 0 0 0 0 0 1 0 0 0 0 542 0 0 Null 2 835 888 1292 2 310 412 302 336 20 0 95 19 WT 2327 205 144 63 1290 66 128 71 49 27 0 92 310 d5 10 66 15 5 22 18 6 20 9 641 0 2 11 d8 2 215 102 31 1 288 166 259 42 47 0 32 4 leiden 13 14 15 16 group Base 5 0 26 23 Naive 1 0 0 0 Null 15 0 15 22 WT 8 2 26 22 d5 59 85 0 0 d8 16 0 3 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 929 556 555 26 7 800 524 504 20 0 178 45 0 Naive 0 0 0 0 0 0 1 0 0 542 0 0 0 Null 872 1259 1251 3 2 476 267 85 37 0 58 206 0 WT 238 90 103 1887 1793 97 86 375 31 0 85 10 2 d5 47 9 6 21 8 19 20 23 670 0 2 1 89 d8 206 143 100 3 2 385 199 26 62 0 24 40 0 leiden 13 14 15 group Base 3 23 27 Naive 1 0 0 Null 11 21 17 WT 8 21 4 d5 54 0 0 d8 12 3 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 609 974 1018 14 8 391 390 515 23 0 209 3 22 21 Naive 0 0 1 0 0 0 0 0 0 542 0 1 0 0 Null 1681 962 487 3 2 822 367 81 33 0 82 11 20 14 WT 107 305 125 1821 1829 48 63 372 28 0 100 8 20 4 d5 4 38 22 23 8 13 18 23 675 0 3 142 0 0 d8 142 200 395 3 2 50 254 33 86 0 26 12 3 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 789 919 17 9 832 696 598 122 19 0 150 0 3 21 Naive 0 0 0 0 0 0 1 0 0 542 0 0 1 0 Null 1425 909 2 3 515 367 300 916 35 0 49 0 12 17 WT 154 287 1847 1861 97 312 85 46 27 0 84 0 8 18 d5 9 45 24 8 20 25 16 13 668 0 2 88 51 0 d8 112 221 3 2 396 172 181 19 63 0 23 0 12 2 leiden 14 group Base 22 Naive 0 Null 15 WT 4 d5 0 d8 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 908 1025 995 516 224 25 185 0 257 0 3 30 21 Naive 0 0 0 0 0 1 0 0 542 0 0 1 0 0 Null 1 1658 900 545 1155 97 39 29 0 97 0 11 17 16 WT 3126 165 301 116 90 488 29 344 0 125 0 8 21 17 d5 21 13 50 20 11 16 670 20 0 5 90 53 0 0 d8 3 136 213 499 176 47 75 9 0 33 0 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 7 1409 1196 709 94 438 24 72 0 8 184 4 32 20 Naive 0 0 0 0 0 1 0 0 542 0 0 1 0 0 Null 1 1090 1054 498 902 228 42 624 0 3 77 11 17 18 WT 3128 390 353 111 43 82 49 37 1 469 120 8 21 18 d5 17 24 43 20 2 17 686 5 0 11 2 141 1 0 d8 3 195 209 451 65 144 88 10 0 0 26 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 12 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 group Base 11 1157 1155 838 266 488 23 0 203 3 31 22 Naive 0 0 0 0 0 1 0 542 0 1 0 0 Null 1 1049 812 791 1497 259 41 0 70 11 17 17 WT 3590 330 396 115 72 105 50 0 115 8 27 22 d5 27 46 26 23 4 21 677 0 3 141 1 0 d8 5 224 165 454 93 146 77 0 26 12 4 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1022 1149 1034 8 9 539 26 0 149 183 21 3 23 Naive 0 0 0 0 0 1 0 542 0 0 0 1 0 Null 2028 1081 637 2 1 276 45 0 33 79 332 12 22 WT 179 302 120 2060 1586 89 30 0 318 86 17 8 21 d5 15 41 26 26 7 15 675 0 15 4 0 144 0 d8 181 206 498 3 2 167 93 0 11 24 6 12 2 leiden 13 group Base 31 Naive 0 Null 17 WT 14 d5 1 d8 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 6 1000 441 1083 838 537 22 0 32 182 4 28 24 Naive 0 0 0 0 1 0 0 542 0 0 1 0 0 Null 2 962 1739 321 491 533 41 0 362 65 11 15 23 WT 3567 298 106 386 137 97 49 0 13 118 8 28 23 d5 26 42 3 19 25 21 683 0 2 2 144 1 1 d8 3 206 152 82 294 325 95 0 8 26 12 3 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 6 979 1072 925 796 20 0 38 142 161 3 33 22 Naive 0 0 0 0 1 0 542 0 0 0 1 0 0 Null 1 1939 1076 540 404 35 0 453 18 53 11 17 18 WT 3522 185 294 132 138 31 0 27 332 118 8 22 21 d5 25 10 37 23 25 680 0 5 16 2 145 1 0 d8 4 194 212 359 293 87 0 10 8 24 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 12 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 group Base 11 644 1165 857 684 576 21 0 182 3 31 23 Naive 0 0 0 0 1 0 0 542 0 1 0 0 Null 1 2129 1083 701 371 126 38 0 66 11 17 22 WT 3555 137 336 110 124 369 31 0 116 8 22 22 d5 25 9 45 21 23 23 679 0 2 142 0 0 d8 3 197 198 339 311 45 71 0 26 12 4 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 9 1113 583 833 742 593 18 69 0 176 3 35 23 Naive 0 0 0 0 0 1 0 0 542 0 1 0 0 Null 1 1018 1680 460 363 288 39 597 0 67 11 18 23 WT 3583 346 122 99 320 110 46 31 0 115 8 28 22 d5 25 46 5 25 12 22 683 4 0 2 142 3 0 d8 3 220 172 463 33 188 77 11 0 24 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 8 840 325 683 802 803 491 23 0 160 3 35 24 Naive 0 0 0 0 0 1 0 0 542 0 1 0 0 Null 2 812 1308 863 597 463 382 39 0 52 11 17 19 WT 3587 312 105 125 269 128 91 45 0 110 8 28 22 d5 25 40 4 17 16 26 17 678 0 2 141 3 0 d8 3 173 121 144 62 298 274 91 0 25 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 25
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 9 1027 738 850 667 244 431 23 0 153 3 29 23 Naive 0 0 0 1 0 0 0 0 542 0 1 0 0 Null 1 1210 756 490 637 1041 292 39 0 52 12 17 18 WT 3609 211 274 141 254 64 67 47 0 112 8 21 22 d5 23 25 43 25 17 3 15 676 0 2 140 0 0 d8 4 178 180 294 52 98 281 78 0 26 12 4 2
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
30 PCs, neigbhor 3 to 18¶
InĀ [6]:
iterate_neighbors(adata, pcs = 30, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 50 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:03)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 40 41 42 43 \ group ... Base 278 164 24 282 289 2 254 12 287 165 ... 55 0 13 19 Naive 0 0 0 0 1 0 0 0 0 0 ... 0 0 0 0 Null 297 517 4 173 162 1 275 1 144 84 ... 19 1 12 14 WT 76 33 623 59 65 604 38 562 96 24 ... 1 0 28 9 d5 24 1 7 14 18 6 7 6 16 7 ... 1 68 0 0 d8 120 28 3 114 102 0 23 0 21 262 ... 19 0 1 4 leiden 44 45 46 47 48 49 group Base 0 0 0 0 0 0 Naive 0 0 0 3 0 0 Null 0 0 0 0 0 0 WT 0 0 4 0 3 0 d5 15 5 0 0 0 3 d8 0 0 0 0 0 0 [6 rows x 50 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 27 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 17 18 19 \ group ... Base 401 8 575 8 225 330 434 355 370 0 ... 71 21 153 Naive 0 0 0 0 0 0 1 0 0 0 ... 0 0 0 Null 844 1 285 1 474 293 212 265 247 0 ... 417 39 57 WT 65 1188 55 942 64 100 54 68 134 773 ... 28 27 118 d5 6 13 9 5 2 28 17 19 26 0 ... 5 370 3 d8 50 5 87 0 111 124 148 107 26 0 ... 18 77 24 leiden 20 21 22 23 24 25 26 group Base 8 45 3 0 35 18 0 Naive 0 0 1 0 0 0 0 Null 4 28 11 0 19 18 0 WT 19 5 8 0 10 29 0 d5 299 1 52 69 0 0 4 d8 4 20 12 0 4 2 0 [6 rows x 27 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 22 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 12 13 \ group ... Base 5 674 653 23 312 447 433 491 309 26 ... 0 56 Naive 0 0 0 0 0 0 0 0 0 0 ... 542 0 Null 0 1090 586 2 821 329 453 347 74 49 ... 0 401 WT 2046 101 200 1380 84 88 47 37 452 36 ... 0 15 d5 12 8 38 17 7 11 9 12 21 663 ... 0 3 d8 0 87 165 2 102 119 38 78 23 77 ... 0 19 leiden 14 15 16 17 18 19 20 21 group Base 215 3 4 37 0 19 2 0 Naive 0 0 1 0 0 0 0 0 Null 86 1 11 19 0 19 2 0 WT 105 129 8 13 0 24 9 0 d5 7 1 61 2 69 0 0 4 d8 33 2 13 4 0 2 1 0 [6 rows x 22 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 6 901 429 619 753 511 25 412 24 88 145 0 226 Naive 0 0 0 0 0 0 0 1 0 0 0 542 0 Null 1 848 1289 700 377 347 3 176 44 621 23 0 86 WT 2369 268 108 102 55 81 1204 45 34 29 381 0 102 d5 13 47 4 13 11 23 18 13 675 9 9 0 5 d8 2 176 125 62 107 339 3 224 79 26 11 0 35 leiden 13 14 15 16 group Base 3 34 0 21 Naive 1 0 0 0 Null 11 17 0 22 WT 8 20 0 24 d5 59 0 70 0 d8 13 5 0 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 6 951 944 551 521 498 29 26 229 0 142 238 4 Naive 0 1 0 0 0 0 0 0 0 542 0 0 1 Null 0 879 1144 1383 359 234 5 45 43 0 339 85 11 WT 2664 270 146 105 71 45 931 37 377 0 24 104 8 d5 11 46 15 9 16 10 10 686 10 0 13 2 139 d8 4 198 93 189 213 333 1 95 15 0 15 34 13 leiden 13 14 group Base 35 23 Naive 0 0 Null 17 21 WT 22 26 d5 2 0 d8 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 7 1033 567 848 515 608 27 28 292 0 211 3 0 26 Naive 0 0 0 0 0 0 0 0 1 542 0 1 0 0 Null 0 978 1335 556 1246 140 3 43 125 0 88 13 0 21 WT 2656 294 103 90 95 426 919 54 27 0 113 8 0 24 d5 14 48 11 22 10 10 9 686 10 0 4 64 80 1 d8 3 193 201 438 64 32 2 98 133 0 26 13 0 2 leiden 14 group Base 32 Naive 0 Null 17 WT 21 d5 0 d8 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 11 1196 964 592 215 611 23 304 0 214 8 3 26 30 Naive 0 1 0 0 0 0 0 0 542 0 0 1 0 0 Null 2 1006 698 1085 1081 450 43 74 0 74 1 12 22 17 WT 3261 334 111 101 59 53 31 444 0 123 259 8 25 21 d5 20 55 25 15 2 6 689 11 0 3 4 139 0 0 d8 3 262 465 67 103 153 90 16 0 31 0 13 2 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 9 560 1120 1052 888 27 261 0 218 4 27 29 2 Naive 0 0 0 0 0 0 1 542 0 1 0 0 0 Null 1 2077 1021 900 253 44 126 0 85 13 23 16 6 WT 3511 105 321 147 453 50 59 0 129 8 25 22 0 d5 21 8 55 28 12 674 12 0 3 156 0 0 0 d8 3 160 202 483 115 100 99 0 29 13 2 3 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 9 1151 804 1001 499 22 310 171 0 6 164 3 28 Naive 0 0 0 0 0 0 1 0 542 0 0 1 0 Null 0 1007 1218 685 1361 40 127 24 0 1 53 12 20 WT 3137 277 133 122 102 32 66 381 0 421 112 8 24 d5 14 46 9 21 13 682 13 13 0 11 3 143 1 d8 3 225 114 413 166 99 137 9 0 0 24 13 2 leiden 13 group Base 29 Naive 0 Null 17 WT 15 d5 0 d8 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 12 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 group Base 9 729 1220 1110 497 23 372 0 173 3 28 33 Naive 0 0 0 0 0 0 1 542 0 1 0 0 Null 0 2145 1114 888 93 47 157 0 69 11 23 18 WT 3533 122 297 131 467 34 75 0 119 8 24 20 d5 17 10 47 25 17 715 14 0 3 119 2 0 d8 3 188 231 428 59 102 156 0 24 12 2 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 1201 7 978 630 638 12 22 339 0 145 163 3 34 25 Naive 0 0 0 0 0 0 0 1 542 0 0 1 0 0 Null 1009 0 878 1377 985 5 40 150 0 19 52 12 17 21 WT 307 2699 139 98 129 891 30 52 0 342 94 8 19 22 d5 47 12 26 11 10 12 683 11 0 15 3 138 0 1 d8 205 3 463 180 85 0 97 123 0 10 25 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 1254 991 612 274 480 22 325 0 3 167 3 27 31 Naive 0 0 0 0 0 0 0 1 542 0 0 1 0 0 Null 0 1040 521 1230 1395 84 41 148 0 1 52 12 23 18 WT 3159 338 116 93 70 392 30 67 0 399 110 8 28 20 d5 15 48 21 4 13 19 682 13 0 8 2 143 1 0 d8 2 216 486 154 63 39 98 109 0 0 23 12 3 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 1202 712 665 921 21 5 0 251 151 198 3 28 32 Naive 0 0 0 0 0 0 0 542 1 0 0 1 0 0 Null 0 1075 1421 1270 498 41 1 0 125 21 57 13 26 17 WT 3027 329 117 127 119 28 537 0 51 321 113 8 33 20 d5 16 47 20 7 20 698 8 0 14 16 4 116 2 1 d8 3 209 51 205 502 94 0 0 89 8 29 12 2 5 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 4 1171 948 245 765 607 15 22 195 0 172 3 24 26 Naive 0 0 0 0 0 1 0 0 0 542 0 1 0 0 Null 1 944 1347 1378 435 287 6 42 23 0 53 12 22 15 WT 2728 312 143 74 106 74 880 32 327 0 109 8 18 19 d5 11 51 9 12 19 15 14 678 15 0 2 141 2 0 d8 2 202 214 39 163 430 0 100 18 0 24 12 2 3 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 6 1174 975 522 961 261 19 24 0 197 3 31 24 Naive 0 0 1 0 0 0 0 0 542 0 1 0 0 Null 0 939 583 1406 612 875 6 36 0 58 12 17 21 WT 2762 326 119 100 330 62 943 46 0 102 8 14 18 d5 10 53 26 12 23 2 15 676 0 2 148 1 1 d8 2 203 549 99 111 101 1 95 0 30 12 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 8 1191 1061 980 356 307 25 18 0 198 3 24 26 Naive 0 0 0 1 0 0 0 0 542 0 1 0 0 Null 0 933 875 560 1203 837 39 9 0 57 12 23 17 WT 3005 331 307 124 86 101 46 689 0 110 8 18 5 d5 13 48 22 26 12 1 691 12 0 2 140 2 0 d8 2 204 126 550 87 95 96 1 0 29 13 2 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1101 5 1199 500 986 16 21 0 117 193 3 25 31 Naive 0 0 0 0 1 0 0 542 0 0 1 0 0 Null 1413 0 934 1503 555 4 37 0 11 57 11 23 17 WT 182 2768 305 102 122 829 28 0 338 110 8 24 14 d5 18 12 54 17 23 12 675 0 16 2 139 1 0 d8 156 2 203 154 544 0 93 0 9 30 12 2 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 30
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 9 1141 903 937 535 337 21 0 179 70 3 27 35 Naive 0 0 1 0 0 0 0 542 0 0 1 0 0 Null 0 900 489 812 1179 1024 39 0 59 7 12 25 19 WT 3549 327 131 163 89 91 29 0 117 284 8 28 14 d5 20 52 25 19 10 2 708 0 2 14 116 1 0 d8 2 197 538 107 105 113 95 0 28 6 12 2 4
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
35 PCs, neigbhor 3 to 18¶
InĀ [7]:
iterate_neighbors(adata, pcs = 35, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 46 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 36 37 38 39 \ group ... Base 9 251 210 301 4 147 18 3 285 148 ... 79 1 1 14 Naive 0 0 0 0 0 0 0 0 1 0 ... 0 1 0 0 Null 1 144 395 228 1 318 1 0 158 340 ... 35 11 0 16 WT 915 38 43 48 678 49 534 551 76 25 ... 9 7 2 26 d5 9 15 24 12 0 4 5 3 4 6 ... 1 36 61 0 d8 2 344 70 103 0 82 3 0 17 17 ... 8 11 1 1 leiden 40 41 42 43 44 45 group Base 21 0 0 0 0 0 Naive 0 0 0 4 3 0 Null 16 0 0 0 0 0 WT 6 10 0 0 0 2 d5 0 0 7 0 0 0 d8 3 0 0 0 0 1 [6 rows x 46 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 25 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 15 16 \ group ... Base 617 14 6 528 276 489 158 461 436 125 ... 31 0 Naive 0 0 0 0 0 1 0 0 0 0 ... 0 0 Null 678 0 1 291 840 275 757 321 311 625 ... 11 0 WT 200 1532 1393 96 56 94 38 60 56 41 ... 326 364 d5 56 10 13 20 11 26 6 7 7 11 ... 7 0 d8 164 2 1 364 41 154 72 103 89 25 ... 4 0 leiden 17 18 19 20 21 22 23 24 group Base 22 16 1 20 1 28 8 0 Naive 0 0 0 0 1 0 0 0 Null 5 73 0 18 11 17 2 0 WT 4 7 0 29 7 13 13 0 d5 269 2 74 0 36 0 0 7 d8 2 18 1 2 11 3 0 0 [6 rows x 25 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 18 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 8 771 575 8 561 711 213 236 618 27 221 0 186 3 Naive 0 0 0 0 0 1 0 0 0 0 0 542 0 1 Null 2 793 929 1 378 391 881 788 207 40 32 0 67 11 WT 2079 174 94 1446 103 108 60 62 79 53 374 0 130 8 d5 16 41 9 15 19 27 14 2 10 675 6 0 3 58 d8 1 174 72 1 400 171 57 96 73 99 17 0 31 12 leiden 14 15 16 17 group Base 22 0 28 9 Naive 0 0 0 0 Null 19 0 17 9 WT 31 0 15 14 d5 1 70 3 0 d8 2 0 3 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 7 909 675 411 37 673 589 435 21 198 0 182 3 Naive 0 0 0 0 0 1 0 0 0 0 542 0 1 Null 0 852 1064 1118 4 329 644 366 37 44 0 53 11 WT 2224 230 109 83 1366 78 72 77 32 398 0 89 8 d5 14 42 6 9 18 20 13 24 673 19 0 3 57 d8 1 193 96 127 5 329 70 235 88 18 0 29 12 leiden 13 14 15 16 group Base 23 0 26 8 Naive 0 0 0 0 Null 17 0 17 9 WT 36 0 15 13 d5 0 71 0 0 d8 2 0 4 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 657 13 790 797 14 610 399 29 357 262 0 200 3 25 Naive 0 0 0 0 0 0 0 0 1 0 542 0 1 0 Null 1196 0 816 483 3 820 789 40 251 46 0 58 11 21 WT 113 1925 172 100 1678 66 79 34 75 431 0 81 8 39 d5 9 10 33 27 15 15 6 674 30 16 0 4 57 1 d8 98 1 136 493 1 84 116 92 125 12 0 32 12 2 leiden 14 15 16 group Base 0 26 15 Naive 0 0 0 Null 0 17 14 WT 0 15 14 d5 72 0 0 d8 0 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 1069 9 842 346 986 20 305 332 29 0 187 2 0 32 Naive 0 0 1 0 0 0 0 0 0 542 0 1 0 0 Null 982 1 453 1355 250 3 791 559 54 0 57 11 0 17 WT 315 2373 113 82 355 1309 62 31 53 0 79 8 0 15 d5 53 11 26 4 15 16 6 12 699 0 4 47 75 0 d8 223 2 508 124 121 0 28 53 99 0 30 12 0 6 leiden 14 15 group Base 25 13 Naive 0 0 Null 20 12 WT 21 14 d5 1 0 d8 2 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 8 1075 1004 910 503 244 26 12 0 150 195 0 2 30 Naive 0 1 0 0 0 0 0 0 542 0 0 0 1 0 Null 1 922 898 483 1208 853 38 3 0 33 66 1 11 17 WT 2849 305 162 123 81 50 27 765 0 299 120 0 8 16 d5 15 60 13 28 16 2 683 14 0 7 4 87 39 0 d8 2 219 120 530 147 47 83 0 0 11 30 0 12 5 leiden 14 15 group Base 24 14 Naive 0 0 Null 20 11 WT 20 5 d5 1 0 d8 2 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 1183 885 628 925 11 12 24 266 0 192 2 24 32 13 Naive 0 0 0 1 0 0 0 0 542 0 1 0 0 0 Null 1038 1533 1258 504 2 2 53 55 0 62 11 21 17 9 WT 308 98 113 112 1920 1707 36 357 0 119 8 24 14 14 d5 49 19 4 25 14 13 702 15 0 4 124 0 0 0 d8 214 155 127 540 1 1 96 25 0 31 12 2 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 1245 1030 627 795 26 184 0 205 3 29 0 30 15 Naive 0 1 0 0 0 0 0 542 0 1 0 0 0 0 Null 2 903 1376 1530 535 44 44 0 65 14 23 0 17 12 WT 3522 324 161 128 107 33 371 0 121 8 26 0 17 12 d5 23 57 13 11 22 683 14 0 4 66 0 76 0 0 d8 2 280 106 186 476 90 16 0 34 13 1 0 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 11 1101 875 823 399 599 19 0 117 180 3 28 30 12 Naive 0 1 0 0 0 0 0 542 0 0 1 0 0 0 Null 2 968 1079 419 1187 725 42 0 28 56 11 22 17 9 WT 3509 322 135 132 112 64 32 0 349 117 8 22 16 12 d5 23 52 13 24 6 13 682 0 13 3 139 1 0 0 d8 2 231 111 510 142 64 89 0 12 28 13 2 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 891 933 841 627 433 21 212 0 156 3 28 30 14 Naive 0 0 0 0 0 1 0 0 542 0 1 0 0 0 Null 2 1871 860 1111 349 182 46 25 0 54 12 24 17 12 WT 3406 164 291 87 101 204 33 380 0 102 8 24 17 13 d5 18 6 51 16 22 14 681 13 0 3 144 1 0 0 d8 2 190 197 95 469 110 91 13 0 22 13 2 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 6 1070 959 555 702 478 24 139 0 183 3 26 36 16 Naive 0 1 0 0 0 0 0 0 542 0 1 0 0 0 Null 1 753 1087 1357 373 800 46 25 0 59 12 23 17 12 WT 3461 269 145 129 107 60 34 446 0 116 8 26 16 13 d5 22 53 11 8 21 11 684 17 0 4 137 1 0 0 d8 2 273 113 165 456 58 84 8 0 29 13 2 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 10 941 394 792 649 480 599 20 0 82 159 3 25 30 Naive 0 0 0 0 0 0 1 0 542 0 0 1 0 0 Null 1 1091 1168 836 344 630 328 41 0 12 54 12 22 17 WT 3537 156 122 97 96 125 163 33 0 333 108 8 25 15 d5 23 14 5 16 20 25 53 680 0 14 4 115 0 0 d8 3 92 145 76 486 110 169 82 0 3 23 13 2 4 leiden 14 group Base 13 Naive 0 Null 9 WT 12 d5 0 d8 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1123 935 442 10 819 9 501 21 0 77 182 3 27 Naive 1 0 0 0 0 0 0 0 542 0 0 1 0 Null 935 968 1382 1 443 3 665 40 0 10 58 12 22 WT 281 161 127 2010 113 1589 54 32 0 290 113 8 26 d5 54 13 9 12 23 13 13 699 0 13 4 116 0 d8 217 96 145 1 549 1 60 87 0 4 28 13 3 leiden 13 14 group Base 36 12 Naive 0 0 Null 17 9 WT 14 12 d5 0 0 d8 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 15 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 11 913 875 418 590 628 20 425 0 87 157 3 28 30 Naive 0 0 0 0 0 0 0 1 542 0 0 1 0 0 Null 2 996 792 1299 779 316 44 216 0 10 52 11 22 17 WT 3551 151 274 119 68 91 31 62 0 309 109 8 28 17 d5 24 12 40 6 15 20 680 12 0 15 3 141 1 0 d8 3 99 183 137 70 464 86 121 0 4 23 12 2 4 leiden 14 group Base 12 Naive 0 Null 9 WT 12 d5 0 d8 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 997 4 495 634 655 619 17 478 20 0 58 150 3 Naive 0 0 0 0 0 0 0 1 0 542 0 0 1 Null 1350 0 1049 699 730 325 3 242 43 0 8 53 11 WT 159 2309 147 221 86 86 1322 68 34 0 274 74 8 d5 12 10 10 57 13 21 16 12 671 0 14 4 128 d8 111 1 158 135 59 452 1 160 89 0 2 22 12 leiden 13 14 15 group Base 26 30 11 Naive 0 0 0 Null 24 17 11 WT 24 14 4 d5 1 0 0 d8 2 4 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 8 1211 1067 500 961 23 196 0 152 3 27 36 13 Naive 0 0 0 0 1 0 0 542 0 1 0 0 0 Null 2 996 1258 1590 528 43 33 0 54 12 23 17 9 WT 3542 310 133 107 150 31 386 0 108 8 28 15 12 d5 23 56 16 9 26 683 15 0 4 136 1 0 0 d8 2 215 139 154 551 87 15 0 25 13 2 4 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 35
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 8 1089 1116 1063 471 24 0 142 180 23 3 26 36 16 Naive 0 0 0 1 0 0 542 0 0 0 1 0 0 0 Null 1 1376 959 567 1312 41 0 26 59 162 11 23 17 11 WT 3550 153 300 149 128 31 0 348 105 3 8 28 15 12 d5 25 16 55 28 10 700 0 14 4 2 114 1 0 0 d8 2 125 200 574 161 89 0 7 28 2 12 3 4 2
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
40 PCs, neigbhor 3 to 18¶
InĀ [8]:
iterate_neighbors(adata, pcs = 40, neighbors = 3, min = 0, max = 18)
computing neighbors
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 47 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:01)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 37 38 39 40 \ group ... Base 39 139 350 246 285 8 0 0 0 19 ... 82 48 77 50 Naive 0 0 0 1 0 0 0 0 542 0 ... 0 0 0 0 Null 7 504 165 200 226 0 0 0 0 31 ... 21 75 52 26 WT 749 32 50 94 86 640 592 582 0 31 ... 51 10 13 21 d5 11 4 13 32 10 8 1 0 0 370 ... 21 7 0 6 d8 2 48 106 108 73 0 0 0 0 78 ... 2 36 15 26 leiden 41 42 43 44 45 46 group Base 32 3 31 1 12 1 Naive 0 0 0 1 0 0 Null 54 1 29 11 9 0 WT 29 1 12 8 11 2 d5 1 88 2 33 0 0 d8 7 1 4 12 1 1 [6 rows x 47 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 27 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 ... 17 18 19 \ group ... Base 4 320 242 357 17 496 0 480 346 291 ... 119 146 32 Naive 0 0 0 0 0 1 0 0 0 0 ... 0 0 0 Null 0 836 720 565 5 286 0 294 231 124 ... 34 61 19 WT 1485 68 49 83 1016 70 949 38 96 40 ... 261 116 15 d5 12 7 5 11 19 14 0 7 39 10 ... 34 3 0 d8 2 48 99 56 4 128 0 55 132 341 ... 12 23 7 leiden 20 21 22 23 24 25 26 group Base 0 2 4 35 21 12 0 Naive 0 1 0 0 0 0 0 Null 0 11 3 25 14 7 0 WT 0 8 42 0 24 3 0 d5 72 36 12 0 0 0 7 d8 0 12 5 1 1 1 0 [6 rows x 27 columns] computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 18 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:00)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:04)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 890 641 11 364 27 556 610 427 380 25 0 196 2 Naive 0 0 0 0 0 1 0 0 0 0 542 0 1 Null 832 1181 2 1286 5 518 344 86 139 37 0 81 12 WT 211 110 1957 83 1630 85 41 401 54 45 0 127 8 d5 44 12 11 9 13 21 16 18 12 666 0 4 57 d8 179 117 1 109 3 173 65 50 384 81 0 27 13 leiden 13 14 15 16 17 group Base 0 31 22 15 0 Naive 0 0 0 0 0 Null 0 16 15 11 0 WT 0 16 22 30 10 d5 85 0 1 0 0 d8 0 4 2 1 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 16 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:05)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 \ group Base 767 940 11 476 732 16 646 31 268 0 234 2 0 35 Naive 0 1 0 0 0 0 0 0 0 542 0 1 0 0 Null 1339 802 0 1064 385 5 738 41 45 0 91 12 0 17 WT 127 237 2033 87 110 1581 68 32 365 0 130 8 0 16 d5 11 42 8 10 28 18 13 678 12 0 6 56 86 0 d8 110 209 1 151 497 1 81 81 16 0 38 14 0 6 leiden 14 15 group Base 24 15 Naive 0 0 Null 15 11 WT 22 14 d5 1 0 d8 2 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 17 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 1040 655 10 797 15 462 217 440 25 0 325 141 0 Naive 1 0 0 0 0 0 0 0 0 542 0 0 0 Null 961 1198 1 438 4 882 734 107 40 0 88 57 0 WT 260 113 2030 116 1636 56 31 408 31 0 23 64 0 d5 43 6 10 28 16 5 10 28 692 0 6 3 85 d8 229 117 2 510 1 60 80 52 84 0 30 23 0 leiden 13 14 15 16 group Base 33 1 23 13 Naive 0 1 0 0 Null 17 11 15 12 WT 16 7 26 13 d5 0 36 1 0 d8 5 12 2 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 925 1119 476 894 9 6 451 22 0 220 1 33 24 17 Naive 0 1 0 0 0 0 0 0 542 0 1 0 0 0 Null 1582 864 1349 469 2 2 113 37 0 90 11 17 15 14 WT 136 276 77 98 1807 1793 419 30 0 131 7 16 23 17 d5 14 49 11 23 13 10 24 689 0 4 131 0 1 0 d8 133 208 134 544 2 1 53 82 0 31 12 5 2 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:01)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 \ group Base 781 9 1065 1078 552 19 439 21 0 166 2 33 23 Naive 0 0 1 0 0 0 0 0 542 0 1 0 0 Null 1706 0 912 654 1067 3 76 42 0 52 11 17 15 WT 143 2627 270 124 87 1036 408 30 0 66 8 16 12 d5 12 12 49 26 16 12 22 687 0 4 128 0 1 d8 122 3 233 542 164 0 15 88 0 23 12 5 1 leiden 13 group Base 9 Naive 0 Null 10 WT 3 d5 0 d8 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:06)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 7 1063 1070 615 547 598 21 18 0 184 3 32 24 15 Naive 0 1 0 0 0 0 0 0 542 0 1 0 0 0 Null 0 846 636 1385 1409 126 42 3 0 57 12 17 19 13 WT 2997 251 113 122 97 410 29 641 0 113 8 16 18 15 d5 13 53 31 6 14 21 673 13 0 4 140 0 1 0 d8 3 249 529 101 140 52 88 0 0 28 12 4 1 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 904 1132 10 1049 782 20 22 0 200 2 27 33 16 Naive 0 1 0 0 0 0 0 542 0 1 0 0 0 Null 2083 1165 0 673 453 3 42 0 81 11 23 17 14 WT 146 235 2515 118 439 1200 32 0 76 8 32 14 15 d5 13 49 13 31 26 17 687 0 3 130 0 0 0 d8 156 265 3 516 127 0 91 0 29 12 3 5 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 15 1164 1229 619 760 23 0 140 170 3 35 25 14 Naive 0 0 1 0 0 0 542 0 0 1 0 0 0 Null 0 1876 955 1071 465 47 0 31 59 12 17 19 13 WT 3568 181 290 141 109 32 1 332 116 8 16 23 13 d5 20 10 46 16 23 701 0 16 3 133 0 1 0 d8 3 160 247 164 487 93 0 8 28 12 5 1 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 14 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 13 group Base 1173 1246 595 14 743 5 21 0 137 186 4 28 35 10 Naive 0 1 0 0 0 0 0 542 0 0 1 0 0 0 Null 1803 907 1192 2 468 0 42 0 31 59 12 22 17 10 WT 175 259 146 2064 97 1609 31 0 307 77 8 31 14 12 d5 13 46 15 18 26 8 692 0 15 4 131 1 0 0 d8 152 251 169 2 493 2 83 0 9 29 12 2 5 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:07)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1210 14 1280 688 573 23 143 0 189 3 30 32 12 Naive 0 0 1 0 0 0 0 542 0 1 0 0 0 Null 2028 0 1033 992 316 39 32 0 62 11 23 17 12 WT 200 3572 184 177 101 30 395 0 109 8 24 18 12 d5 15 20 38 29 21 687 16 0 3 139 1 0 0 d8 191 2 312 172 376 85 19 0 32 12 2 5 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:04)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1159 16 855 1045 737 24 0 143 147 2 27 32 10 Naive 0 0 0 1 0 0 542 0 0 1 0 0 0 Null 2214 0 977 758 434 45 0 28 51 11 20 17 10 WT 192 3624 264 143 101 33 0 332 82 8 25 14 12 d5 11 21 48 24 25 714 0 13 3 109 1 0 0 d8 188 2 179 213 489 89 0 7 23 12 2 5 0 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:02)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:01)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1158 1317 6 950 23 329 22 181 0 147 2 30 32 Naive 0 1 0 0 0 0 0 0 542 0 1 0 0 Null 2238 1165 0 507 4 467 38 43 0 52 11 23 17 WT 199 175 2422 111 1308 110 32 353 0 73 8 25 14 d5 11 30 13 27 15 33 688 19 0 2 130 1 0 d8 217 217 1 514 1 108 86 23 0 23 12 2 5 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 12 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 group Base 1189 15 1465 1076 24 151 0 200 2 28 33 14 Naive 0 0 1 0 0 0 542 0 1 0 0 0 Null 2353 1 1315 684 47 33 0 70 12 22 17 11 WT 211 3573 333 132 33 346 0 120 8 31 18 25 d5 12 19 54 31 697 19 0 3 133 1 0 0 d8 220 2 294 532 94 18 0 29 12 2 5 1 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:02)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1184 1464 1078 16 2 20 160 0 195 2 27 35 14 Naive 0 1 0 0 0 0 0 542 0 1 0 0 0 Null 2382 1298 668 3 0 47 32 0 73 12 21 17 12 WT 215 336 126 1940 1705 31 329 0 88 8 25 14 13 d5 10 57 27 18 9 694 18 0 4 131 1 0 0 d8 225 290 532 2 0 93 17 0 29 12 2 5 2 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 13 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 11 12 group Base 1106 1260 1046 5 10 349 21 149 0 189 2 25 35 Naive 0 1 0 0 0 0 0 0 542 0 1 0 0 Null 2162 1040 622 0 4 548 44 31 0 64 12 21 17 WT 185 281 131 1838 1813 76 30 343 0 82 8 29 14 d5 9 49 28 8 16 9 699 15 0 4 131 1 0 d8 199 251 528 1 1 89 86 7 0 28 12 3 4 computing neighbors
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
using 'X_pca' with n_pcs = 40
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:03)
running Leiden clustering
finished: found 11 clusters and added
'leiden', the cluster labels (adata.obs, categorical) (0:00:03)
running PAGA
finished: added
'paga/connectivities', connectivities adjacency (adata.uns)
'paga/connectivities_tree', connectivities subtree (adata.uns) (0:00:00)
--> added 'pos', the PAGA positions (adata.uns['paga'])
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:08)
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
/opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1207: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead if not is_categorical_dtype(values): /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:1216: FutureWarning: The default value of 'ignore' for the `na_action` parameter in pandas.Categorical.map is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning color_vector = pd.Categorical(values.map(color_map)) /opt/conda/lib/python3.10/site-packages/scanpy/plotting/_tools/scatterplots.py:391: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored cax = scatter(
leiden 0 1 2 3 4 5 6 7 8 9 10 group Base 1198 15 1471 1103 23 148 0 172 2 29 36 Naive 0 0 1 0 0 0 542 0 1 0 0 Null 2392 1 1313 678 46 28 0 57 12 21 17 WT 216 3604 340 135 32 338 0 114 8 29 14 d5 12 18 60 30 721 18 0 3 107 0 0 d8 227 2 284 543 91 16 0 28 12 1 5
/scratch/local/20367147/ipykernel_1279247/2632075354.py:25: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.
print(obs_df.groupby("group").value_counts().unstack())
InĀ [9]:
# End of Notebook
print("\nNotebook Ends")
Notebook Ends